Gene encoding prenyltransferase and recombinant plasmid carrying the same

ABSTRACT

A novel PSL family prenyltransferase has relaxed substrate specificity, which can use a variety of cyclic dipeptides and prenyl donors as substrates to produce various terpenylated diketopiperazines. An amino acid sequence of the prenyltransferase is SEQ ID NO: 1. An application of the prenyltransferase is transferring different prenyl groups to Trp-containing cyclic dipeptides. The prenyltransferase catalyzes the formation of terpenylated diketopiperazines by assembling prenyl groups onto cyclic dipeptides, which provides a new strategy for drug development of diketopiperazines.

CROSS REFERENCE OF RELATED APPLICATION

This is a continuation application of U.S. patent application Ser. No. 17/042,942, filed on Sep. 29, 2020; and claims the priority of Chinese Patent Application CN 201810831718.3, filed to the China National Intellectual Property Administration (CNIPA) on Jul. 26, 2018, the entire content of which are incorporated hereby by reference.

BACKGROUND OF THE PRESENT INVENTION Field of Invention

The present invention relates to a technical field of genetic engineering and biopharmaceuticals, and more particularly to a novel phytoene-synthase-like (PSL) family prenyltransferase and its applications.

Description of Related Arts

Prenylated secondary metabolites are widely distributed in bacteria, fungi and plants, such as indole alkaloids, flavonoids, and quinones. The introduction of prenyl moieties not only greatly enriches the structural diversities of natural products, but also increases the biological activities of these compounds by enhancing their affinity for membranes as well as the interactions with cellular targets. The studies of structure-activity relationships have shown that the biological activities of prenylated aromatic compounds is generated from the prenyl substitutions. Due to the structure diversities of prenylated natural products, it is difficult to synthesize them via chemical methods. The use of prenyltransferases with substrate promiscuities as tool enzymes provides new strategies to generate novel prenylated derivatives in drug discovery applications.

Aromatic prenyltransferases catalyze the transfer reactions of prenyl moieties from different prenyl donors, e.g. dimethylallyl (DMAPP), geranyl (GPP), farnesyl (FPP), or geranylgeranyl (GGPP) diphosphate, to various aromatic acceptors to form active molecules with multiple biological functions in the biosynthesis of both primary and secondary metabolism of living organisms. The phytoene-synthase-like (PSL) family prenyltransferases are newly discovered, which use aromatic compounds as substrates. Phylogenetic analysis shows that they form the same branch with phytoene synthases instead of typical aromatic prenyltransferases. The only PSL family prenyltransferase reported so far is NzsG involved in the biosynthesis of neocarazostatin from Streptomyces sp. MA37, which has strong substrate specificity for both the prenyl donor as well as the prenyl acceptor and can only transfer dimethylallyl pyrophosphate (DMAPP) to precarazostatin.

SUMMARY OF THE PRESENT INVENTION

An object of the present invention is to provide a novel phytoene-synthase-like (PSL) family prenyltransferase with relaxed substrate specificity, which can use a variety of cyclic dipeptides and prenyl donors as substrates to produce terpenylated diketopiperazines.

Firstly, the present invention provides a prenyltransferase, comprising:

a) a protein whose amino acid sequence is SEQ ID NO:1; and

b) a protein, which has prenyl transfer activity of a), obtained by deleting, substituting, inserting or adding one or more of amino acids in a).

A gene encoding the above prenyltransferase is provided, a nucleotide sequence of the gene is SEQ ID NO:2.

The present also provides a recombinant plasmid carrying the above gene.

An application of the prenyltransferase of the present invention is in transferring prenyl donors to cyclic dipeptides.

The prenyl donors are dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP), farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP).

The cyclic dipeptides are cyclo (L-Trp-L-Xaa), wherein Xaa is Val, Pro, Leu, Ile, Ala, Thr, Gln, Phe or Tyr.

The prenyltransferase of the present invention produces terpenylated diketopiperazines by assembling prenyl groups onto cyclic dipeptides, which provides new tool enzyme for combinatorial biosynthesis of prenylated diketopiperazines (DKPs) which are meaningful for new drug research and development.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a construction verification of a recombinant plasmid of the present invention;

FIG. 2 is a SDS-PAGE analysis of purified DmtC1 of the present invention;

FIG. 3 is a high-performance liquid chromatography (HPLC) traces of DmtC1-catalyzed reactions using different cyclic dipeptide substrates according to the present invention;

FIG. 4 is a high-resolution mass spectrum (HR-MS) of pre-DMT C according to the present invention;

FIG. 5 is a high-resolution mass spectrum (HR-MS) of pre-DMT G according to the present invention;

FIG. 6 is a high-performance liquid chromatography (HPLC) traces of DmtC1-catalyzed reactions using different prenyl donors according to the present invention;

FIG. 7 is a high-resolution mass spectrum (HR-MS) of cWP-GPP according to the present invention;

FIG. 8 is a high-resolution mass spectrum (HR-MS) of cWP-GGPP according to the present invention.

FIG. 9 is a half inhibition rate of pre-DMT C on VSV according to the present invention.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

Referring to the drawings, the present invention will be further illustrated.

Embodiment 1: Gene Clone of Isopentenyl Transferase

1. Extraction of Genomic DNA

Streptomyces youssoufiensis OUC6819 was cultured in liquid TSBY medium (3% tryptic soya both, 10.3% sucrose, 0.1% tryptone, 0.05% yeast extract) at 30° C. for genomic DNA extraction. Cells were harvested by centrifugation (1 min, 17000×g), and washed (1 mL of STE buffer). 500 μL of lysis solution (3-5 mg/mL lysozyme in STE buffer) was added and incubated at 37° C. until cells became translucent; 250 μL of 6% SDS was then added with further incubation at 37° C. until cells became clear; after addition of ten percent 3 M NaAc (pH 4.8) and 200 μL of a mixture of phenol: chloroform: isoamyl alcohol (25:24:1; v/v/v), the sample was rotated end-over-end for 10 min; after centrifugation (5 min, 17000×g), the aqueous phase was transferred with wide bore pipet into a clean tube. DNA was precipitated by equal volume of isopropanol and spooled using a sealed Pasteur pipet before being transferred into a microcentrifuge tube and rinsed with 70% ethanol. The air-dried DNA was dissolved in a minimal volume of TE buffer for subsequent use.

2. Construction of the Recombinant Plasmid pET32a-dmtC1

A primer pair was designed: P1: 5′-CCGGAATTCACCCGCCAGGAAATGGACG-3′/P2: 5′-CCGCTCGAGCGTCGAGTCGGCGGTCAGGG-3′. The gene dmtC1 was amplified by polymerase chain reaction (PCR) using primer pair P1/P2 from genomes of S. youssoufiensis OUC6819. Genomic DNA was diluted by 10 times as a template for PCR.

PCR Reaction System:

Primer pair P1 and P2 5 μL (50 pmol) each, template 5 μL, 10×Reaction Buffer 10 μL, 2.5 mM dNTP 10 μL, 25 mM MgCl₂ 6 μL, pfu DNA Polymerase 1 μL (5 U/μL), adding ddH2O to 100 μL.

PCR Steps:

Each cycle of PCR includes steps for template denaturation, primer annealing and primer extension. The initial step denatures the genomic DNA by heating it to 98° C. for 10 s. In the next step of a cycle, the temperature is reduced to 66.3° C. for 15 s. Finally, the synthesis of new DNA begins as the reaction temperature is raised to 72° C. for 10 s. After 28 cycles, the amplified product was digested with EcoRI and Xhol, and ligated into pET32a resulting in pET32a-dmtC1 which transforming into Escherichia coli DH5a. Positive clones were screening by using enzyme digestion. Results are shown in FIG. 1 (panel iii), wherein target fragment with expected size was obtained. The verified clone was sequenced, wherein a nucleotide sequence of the gene is SEQ ID NO: 2, and an amino acid sequence of the encoded protein is SEQ ID NO: 1.

3. Expression and Purification of DmtC1 in Escherichia coli

10 mL overnight culture of E. coli BL21 (DE3) harboring DmtC1 expression plasmid was inoculated into 1 L of LB medium (containing 50 μg mL⁻¹ ampicillin) and grown at 37° C. with shaking. Expression was induced at an OD600 of approximately 0.6 by addition of IPTG (0.05 mM final concentration), and cultivation was continued for additional 16 hrs at 16° C. The cells were pelleted by centrifugation (15 min at 8000×g) and resuspended in 30 mL of binding buffer A (0.05 M Tris-HCl, 0.5 M NaCl, pH 7.5, containing cOmplete™ protease inhibitor cocktail). The resuspended cells were lysed by sonication in an ice-water bath with an ultrasonic processors VCX750 (Sonics and Materials Inc, PA, USA), and centrifuged at 10,000×g for 30 min at 4° C. The supernatant was applied to a HisTrap HP column (1 mL, GE Healthcare) and the His-tagged DmtC1 protein was eluted with a linear gradient of imidazole (30-500 mM) in the binding buffer using an ÄKTA Purifier system. After SDS-PAGE analysis, fractions containing pure DmtC1 were pooled, concentrated and exchanged to Tris buffer (0.025 M Tris-HCl, 0.02 M NaCl, and 10.0% glycerol, pH 7.5) by using Amicon Ultra-15 30-kDa cutoff centrifugal concentrator (Millipore) and stored at −80 for subsequent use.

Embodiment 2: In Vitro Assay of DmtC1

The enzymatic assay of DmtC1 was carried out in 50 mM Tris-HCl buffer (pH 8.0) with 2.5 mM MgCl₂, containing 10 μM DmtC1, 1 mM DKP, and 0.2 mM FPP. The optimal assay conditions were obtained at 30° C. After 1 hr, the reaction was quenched by the addition of equal volume of methanol and mixed by vortexing. The mixture was centrifuged at 17,000×g for 20 min to remove protein.

The supernatant was then subjected to HPLC analysis using a YMC-Pack ODS-AQ C18 column (150 mm×4.6 mm, particle size of 5 μm, pore size of 120 Å) under the program: phase A consisting of 0.1% (v/v) formic acid and ddH2O, phase B consisting of 0.1% (v/v) formic acid and acetonitrile; 10% B (0-5 min), 10% to 50% B (5-15 min), 80% to 100% B (15-25 min), at a flow rate of 1 mL min⁻¹ and UV detection at 300 nm. As shown FIG. 3, a new absorption peak appeared after the reaction, indicating that the enzymatic reaction occurred.

The obtained product was subjected to high resolution mass spectrometry (HR-MS) analysis (FIGS. 4-5). From the MS spectrum (FIG. 4), [M+H]⁺ of compound 3 in panel ii is 488.3274, which is consistent with molecular weight of pre-DMT C ([M+H]⁺ calcd 488.3232); [M+H]⁺ of compound 4 in panel iv is 490.3429, which is consistent with molecular weight of pre-DMT G ([M+H]⁺ calcd 490.3389) (FIG. 5).

Embodiment 3: Probing Substrate Promiscuity of DmtC1

When cWP was used as the substrate, the FPP in the enzymatic assay in the embodiment 2 was replaced with DMAPP, GPP or GGPP. HPLC (FIG. 6) and HR-MS analysis (FIGS. 7-8) were performed after the reaction is terminated. [M+H]⁺ of compound 5 in panel iii is 420.2647, which is consistent with molecular weight of GPP-cWP ([M+H]⁺ calcd 420.2606) (FIG. 7); [M+H]⁺ of compound 6 in panel v is 556.3896, which is consistent with molecular weight of GGPP-cWP ([1\4+H]⁺ calcd 556.3858) (FIG. 8). It is proved that DmtC1 displays broad substrate specificity regarding to the prenyl donors and could be a powerful biocatalytic tool enzyme for combinatorial biosynthesis of terpenylated diketopiperazines.

Embodiment 4: Anti-Vesicular Stomatitis Virus (VSV) Assay of Compound 3 of the Embodiment 2 1. Experimental Samples and Experimental Methods

A sample solution to be tested was compound 3 separated from the embodiment 2. A solution of a required concentration was prepared with DMSO for testing activity.

African green monkey kidney cell line Vero cells were spread on a 96-well plate at 5000/well and cultured in DMEM culture medium for 12 hrs; the vero cells were pretreated with the compound 3 for 1 h with gradient concentrations, and then VSV-GFP viruses were used to infect the cells at M.O.I=0.01 for 1 h; the medium containing compound 3 was then replaced to continue cultivate for 16 hrs; average fluorescence intensity was counted and half inhibition rate (IC₅₀) of the compound 3 on VSV was calculated.

2. Experimental Results and Conclusions

The compound 3 has a significant inhibitory effect on VSV, and IC₅₀=2.66 μM (FIG. 9).

INDUSTRIAL APPLICABILITY

In the process of studying the biosynthetic machinery of drimentines in Streptomyces youssoufiensis OUC6819, the PSL prenyltransferase DmtC1 with broad substrate specificity was discovered. In vitro biochemical experiments have shown that DmtC1 has a broad spectrum of substrates, and can use a variety of cyclic dipeptides and prenyl donors as the substrates to produce terpenylated diketopiperazines. The relaxed substrate specificity displayed by DmtC1 would enable potential generation of an array of structurally diverse terpenylated diketopiperazines, which are meaningful for new drug research and development. 

What is claimed is:
 1. A method for assembling prenyl groups onto cyclic dipeptides, comprising using a prenyltransferase for assembling the prenyl groups to Trp-containing cyclic dipeptides; wherein the prenyltransferase comprises an amino acid sequence of SEQ ID NO:1.
 2. The method, as recited in claim 1, wherein the cyclic dipeptides are cyclo (L-Trp-L-Xaa), wherein Xaa is Val, Pro, Leu, Ile, Ala, Thr, Gln, Phe or Tyr.
 3. The method, as recited in claim 1, wherein the prenyl groups are dimethylallyl pyrophosphate, geranyl pyrophosphate, farnesyl pyrophosphate or geranylgeranyl pyrophosphate. 